Mass Genesis
by Ronnel no Fenniksu
Summary: Humanity has a secret. A century and a half before they discovered mass effect technology, the key to the galaxy for them; they were nearly wiped out by attackers from beyond the stars. How they overcame this, has given the galaxy a new genesis when it should be on its final chapters. How will the other races react?
1. Prologue

_**Prologue**_

Humanity had a secret, one never even hinted to the other races that they had met since reaching out to the stars. Long before they made it to Mars, and found the key to the galaxy entombed for millenia there...

Mankind was almost wiped out, by an extraterrestrial assault. Strike after strike wore down one of the megacities, the bastions of humanity on Earth, wearing away at it. If they had succeeded, then not just that city, but all life on earth would have been obliterated, no trace left at all. And if that had happened? Well, let's not worry about that. Because thanks to the valiant struggle of a noble few, controlled by a puppetmaster who served a cause he didn't even know of – a cause that the lynchpin of Humanity's defenders unknowingly thwarted – Mankind was saved from annihilation, on the eve of their destruction.

But this was not so easy. The final attack – carried out by the puppeteer, not the invaders at all – caused a deep wound on Earth's inhabitants. A motley of warring nations, held by truce and peace, wouldn't be able to protect themselves any more, not with the drastically reduced numbers that they were left with. No, something more would be needed, more unified, stronger.

And they had the keys. Biomechanical juggernauts, and insanely advanced technology, paved the way to a global economy that was far more robust than had even been known on Earth before. Bio-technology became commonplace. But the culture, though vibrant and full of life, was a thin veneer of civilization, over the steadfast determination to never fall to attackers again, to never fail in the face of those who would destroy them. Weapons and defense technology took a massive boost forward, based largely on what was developed to counter the foes that had come so close to killing Humanity, as well as the Juggernauts themselves – the EVANGELIONS.

Biomechanical combat units, as tall as skyscrapers, armed with the ability to create what was known as an 'Absolute Terror Field' which countered the similar field of the invaders, which gained the designation of 'Angels'. Built to be humanoid, based on the flesh of the original, conquered and captured Angels – which came to be known as 'Adam and Lilith' – and armed with the strongest machinery, created specifically to fight the monstrous invaders who sought to destroy Humanity. Pilotable mecha, like something from an old anime or cartoon, but the requirements to be a pilot – at least originally – were so horrendous that none who knew of it had clean consciences. For to be a pilot, a guardian spirit was needed.

After all the EVANGELIONS were originally partially grown from the flesh of alien beings that sought to kill Humanity. To keep the alien spirit from killing any pilot, something was needed to shield them. Thus came the requirement... that the pilot's parent – preferably mother, as most EVA were based on Adam, a 'masculine' entity – be sacrificed, absorbed into the EVANGELION unit a child was to become the controller of.

Only six originally knew of this terrifying restriction. Of those six, one only learned much later. Three were absorbed into the EVANGELION – two so that their son and daughter could later pilot the EVANGELION to fight the Angels that were coming, the third so that the third pilot would have a protective spirit, even though the woman was not the child's real mother.

So it was that three children became the unknowing shield for humanity, guided by the puppeteer – the fourth person who knew, a man known as Gendo Ikari – formerly Rokubungi – the father of the male pilot. There was no preferential treatment – in fact, the son was banished from the father's presence, just after the boy had lost his mother.

But he was called back, when the Angels began their assault. He became the lynchpin, and in the end, the one who stopped his father's heinous plan for Humanity. To learn of their struggle, the losses they suffered, the triumphs that they brought about, would take a work of its own. But instead, we are here to talk about what happened when Humanity reached out to the stars, and found themselves no longer alone.

What I have just told you, is Humanity's secret. No non-Human knows of EVANGELION, of the struggle against the Angels. What they do know of, is the results.

A culture that is strangely divided – at once both incredibly militant, with technology far beyond what they should have, and yet relaxed and unconcerned of invasion or attack. This is because they do not know that, after what happened when Humanity reached out – Relay 314 – more EVANGELION were commissioned, and stationed to be the guardians of Humanity wherever it might be. How they got pilots will be revealed at another time.

But how did Humanity's grand secret change things for them when they reached the intergalactic stage? To tell that tale, the start of this one, requires... a more personal, shall we say, approach? Data is all well and good, but its the story of the people involved who truly make history come alive for us, isn't it? After all, this is the start of Humanity's Mass Genesis.

_**END PROLOGUE**_

_**AN: Well, this is going to be interesting. The works being used here are, obviously, Mass Effect – and Neon Genesis Evangelion, an older, but quite good in my opinion, mecha anime from the nineties. I don't know how long I'll maintain the creative spark for this story, but I hope it's at least long enough to entertain people! I'm posting this chapter, the prologue, up at the same time as the first chapter, as this just serves as a base grounding for Evangelion for the people who may not know it. **_

_**Also, as to where my Shephard in this story is going to come from. He's going to end up being a 'Spacer' born man, meaning his mother is still in the picture serving in the USN, non-biotic, working as a straight Soldier. Which of the backgrounds he'll have I haven't decided yet though. **_


	2. Chapter 1

_**Chapter 1: God Is In His Heaven**_

_Citadel_

_Human Embasssy_

Councilor Donnel Udina crossed his arms as he stared at the two military men standing in front of his desk, and sighed. Floating in the air above his desk was the projection from his holo-terminal, showing various dossiers of soldiers. The first one was his choice, one of the two females in the selection, and with the ruthlessness to carry things out no matter the price.

"What about Lieutenant Trace? Born on Mindoir, joined up at an early age." It was the more decorated soldier on the other side of his desk – not that the soldier gave a damn about said decorations – who shot that proposal down.

"Not a chance. Too many people remember just why she left Mindoir. And what she did to the Batarians in response to that. She's not called the Butcher of Torfan for nothing, the four-eyes are still known to leave a system where she's been spotted if they can." Admiral Steven Hackett, the man in charge of the Arcturus Fleet, Humanity's single largest fleet, had to resist the urge to roll his eyes at the suggestion. While the girl fit one of the most important criteria for what they wanted, having her as the selection would... give the other races reason to believe that Humanity viewed them negatively. Which was why Udina wanted her for the job – he did have that harsh view, but unfortunately he had somehow managed to get to the position of power he had now, and it was too hard to oust him from it. Instead he countered his plans, placing his own suggestion.

"But Ashon might fit the bill. Joined up at an early age just like Trace so there's that, but he's known as the Hero of Elysium. Damn well fits it too, holding those colonists together until we were able to get insystem to wipe out those damnable pirates." Despite their youth, the two named were big names, not just for Humanity, but for the other races. Both had seen a truly noteworthy event in their life, which shaped them, and had brought them to the public's eyes, even if it wasn't for the best of reasons, as in Trace's case.

"Sorry sir, but Ashon isn't a possibility. She's Earthborn, with no record of her family, so there's no chance of her filling one of the most absolutely critical requirements. You should know that as well as both of us do." Now the third man spoke – Captain David Anderson, and though he didn't know it, the supporter of the only possible candidate for the job that was open that the other two men could ever agree on. There were others, not countless, but they were there, but for one reason or another either Udina or Hackett would veto them all, all of the candidates except...

"However, Shepard does fill all of the requirements we have. He's a born Unnie brat, his mother was Captain Hannah Shepard from the _Carl Jung_, recently diagnosed with a terminal bone cancer from overexposure to raw element zero back before we had proper safeguards. Her son isn't a Biotic though, but he's a damn fine soldier if I ever met one." Anderson's words were met with silence from the other two men, which made him only slightly nervous. After a few moments though, Udina moved back to his chair and sank down into it, steepling his fingers in front of his face.

"Shepard Jr? Isn't he the one that they've taken to calling the 'Sole Survivor' or some such nonsense?" Despite the callous words, the counselor's eyes were gleaming with interest. The captain took this as his chance to go on.

"Yes, Commander Shepard has earned that unfortunate misnomer from the fact that he is the only one from his squad to survive the terrors of what happened on Akuze." As he said that, both Naval officers' fists clenched at the thought of what had happened on that lonely little planet. But Anderson plowed onwards. "However, he has recently made it through the psych-evals for post-traumatic stress, and he seems to be coping fairly well. He's managed to get a handle on the death wish he exhibited shortly after Akuze, though it has left him a bit... blunt at times. At other times he seems overly willing to see the good in those around him, almost to a fault, though I've never known his judgment to be wrong." As he spoke, both Udina and Hackett were nodding their heads. They'd read the dossier on Commander Leon Shepard, though both had put him aside as their second choice after their primary picks. Now that all three had been broached though...

"The only problem I see is that the galaxy at large doesn't know him that well. While Humanity does, he isn't that well known outside of the Unified Navy." This came from the fleet commander, who had a thoughtful look on his face. What he wasn't expecting was for Udina to suddenly leap up, crashing his right fist into his left palm with a short cry of exultation.

"Don't you see though Admiral? That's _exactly_ what Humanity needs! We're the newcomers to the galactic stage, the relative unknowns! Why should we have anyone BUT a skilled, qualified, talented unknown as our first Spectre? It would give interesting parallels to anyone who could discern it, and while the common masses might not, I assure you that those in power most certainly would!" As he spoke, Udina could see that he was winning Hackett over.

"And if you're worried about him being skilled enough sir, the Commander did graduate top of his class from the E7 program. He's also gotten cross training in the unique piloting for the final job requirement, and if his mother knew..." Anderson trailed off, looking at Hackett, who knew Hannah from back when the Arcturus fleet had been a fraction of its size. The admiral sighed and nodded.

"Not only would she not hesitate, she'd demand to know why consideration of her even slowed us down. She's desperate for some way to make a difference, has been since the doctors finalized her prognosis. This just..."

"Exactly. Shepard's the best suited for the job, hands-down. He's the only choice." Then Udina noticed something in his file that made the man start laughing, a footnote that had managed to escape all of their notice buried as it was under the minutae of explanations.

"We chose better than we knew gentlemen. Our boy Shepard might possibly be an Ikari. It's not listed on his file proper because his mother was never sure who the father was, but there you go. The blood of the defender comes forth once more." All of the men in the room let out a soft chuckle, equally amused by that little revelation. Udina then turned his gaze to Anderson.

"Right, your his CO. You get to break the news to him, I'll make the call to the Council authorities and let them know we have a candidate for evaluation. You have the mission specs for what you'll be doing?" As Anderson nodded, Hackett leaned forward.

"Be careful with this one Anderson. Kryik isn't another Arteruis, don't make the mistake of thinking he is. We might not like the Turians but we can damn well work with them." Anderson straightened up and saluted Hackett, who returned the salute. "Dismissed soldier. Let our boy know of his bright and harrowing future."

"Sir!"

_Earth Nearspace_

_UNSV Normandy_

Commander Leon Shepard was standing behind the pilot's chair in the forward portion of the _Normandy_, staring down at the planet that his race called home. They had been through a lot – with several billion people dying during the turn of the century, but they had managed to overcome that, had managed to somehow make it back to around five billion people by the time that they had discovered the Prothean ruins on Mars. Their technology, combined with human bioengeneering, had pushed humanity centuries ahead of where they once would have been. Even now, the ship that they were standing on, was one of the pinnacles of that technology.

Shaking himself from his musings he leaned over and rested one hand on the back of the pilot's chair, trying to grasp what the pilot was doing, and understand the differences between piloting one of their interstellar starships and the piloting that he had been trained in. The pilot, whom Leon had learned was called Joker by nearly everyone who knew him, flicked one eye up at the commander leaning over him, then the other to his nominal co-pilot, then to the person who walked in behind Shepard. Shaking off the small audience that he had somehow gained, Joker focused on his job.

"Thrusters, check. Navigation, check. Flight plan authorized. We are a go." The ship shuddered as they approached the Charon Relay, making the transition between real-space and the inexplicable reality that existed in between the Relays. A few moments later there was another shudder as they returned to normal reality. "Internal emissions sink online and running fine sir. Everything's running as smoothly as it did in testing." Shepard straightened up, nodding. "Drift is just under 1500k units, within tightline parameters. On route to destination."

"1500 is good. Your captain is good." The strange, flanging voice of the final person on the bridge was discordant to the humans, who even after years were still trying to get a grip on good relations with one of the other races that they had encountered. With that comment, the Turian Nihlus Kryik turned and left the cockpit. As soon as the door sealed behind him, Joker let out a snort.

"I hate that guy."

"He gave you a compliment... so you hate him?" This came from his co-pilot, Lieutenant Kaiden Alenko. Leon took a step back and clasped his hands behind his back in the at-ease position as he waited to hear Joker's response.

"You remember to zip up after hitting the head? That's good. I just jumped us lightyears from earth and hit a target comparably the size of a pinhead? That's fantastic!" The pilot lost the jokingly dismissive tone in his voice as he continued. "And in any case, Spectres are trouble. I don't like having him onboard my baby here. Call me paranoid."

"Calling it. The Council has every right to have someone keeping an eye on things on a brand new class of warship which might change the makeup of fleet doctrine for every race. I'd rather have someone who knows how to handle things, over some engineer who wouldn't know how to apply things he saw to the bigger picture." Alenko leaned back in his seat as the auto-pilot brought them closer to their destination.

"Yep, that's the official story. But only a blind man believes the official story."

"They don't need a Spectre on a shake-down cruise." Leon's two cents made both of the pilots jump in their seats a little, having thought that the Commander had left when Nihlus did.

"See, even the XO agrees with me! There's more going o-"

Before Joker could finish the intercom buzzed to life, ringing with Captain Anderson's voice. "Joker, status report!" Leon had been serving under Anderson for over a month now, transferring onto the Normandy at the same time as his Captain did, since according to the man, it was _'too damn hard to train a good XO, why should I give up the one I've got now?'_

"Just cleared the Relay sir. Stealth systems are nominal, everything's running fine." Joker responded.

"Good. Find a comm. buoy and link us to the system. I want mission reports back to the USN chiefs as soon as we reach Eden Prime."

"Aye aye sir. Better brace yourself too captain, Nihlus just left, think he's on his way to you."

"He's already here Lieutenant." Joker shook his head as Kaiden grinned at that. "If Shepard is there, tell him to meet me in the comm room for a briefing. Anderson out." The intercom cut off as Joker turned to look at Shepard.

"You get all that Commander?"

"I'm on my way." Leon was heading to the door as he heard Joker start talking again.

"Is it just me, or does the captain always sound pissed off?"

"Only when he's talking to you Joker." Whatever Joker said in response to Alenko was cut from Leon's hearing as the door slid shut behind him. As he walked through the command room, he heard one of the soldiers talking to the ship's chief medical officer, saying that he had grown up on Eden Prime, and that there wasn't much call for a stealth-capable ship in this area. As the CMO shrugged, Shepard had to resist the urge to snort.

_Stealth isn't all that makes this weird kid. Though I don't know why they decided to send a heavy frigate on a simple run to Eden either, it'd make more sense to have us skirting the edge of the Terminus. That'd give us a chance to see how good the modified AT shields are too._ As he thought, Leon had reached the communications room, and he blinked when he saw that only Nihlus was in the room, staring at a screen that had a view of Eden Prime pulled up on it. He could have sworn that Anderson said he would be here, but maybe he had stepped out for something before Shepard got there.

"Ah, Commander Shepard." Nihlus turned around to look at Leon as he entered the room. "I was hoping you would get here first, it would give us a chance to talk." Leon raised one dark brown eyebrow at that.

"About?" The Commander was curious as to what a Spectre could possibly want with him, and wondering just what was going on. He could remember Anderson saying that Nihlus was with him, but what the Turian had just said implied something else entirely, which was mildly confusing – and possibly a bit worrisome as well.

"I'm interested in this world we're going to, Eden Prime. I hear it's quite beautiful."

"I'm the wrong person for that then. I've never been there, spent most of my time either on ships or on stations. But they do say it's a paradise here." What Shepard couldn't say was that the colony was just a few thousand people away from the cap that would get them their first trio of Eva guardians, which were already in construction back on Earth in anticipation of that happening.

"Yes, a paradise. Serene, tranquil, safe." That proved to Shepard that the Spectres didn't know everything – no human felt truly safe unless there was at least one Eva nearby, in case things went out of control. But that wasn't spoken of to the alien races, ever. "Eden Prime has become something of a symbol for your people. Proof that Humanity can establish colonies around the galaxy, and even more, keep them protected." His tone was friendly, but suddenly turned much darker. "But how safe is it really?"

That set offseveral warning bells in Shepard's head. "Do you know something?" Like that the colony doesn't have its final defenses yet? As Leon prepared to leap at the Spectre, who had turned back to look at the display again, the Turian spoke.

"Your people are still newcomers Commander. The galaxy can be a truly dangerous place. Are the Unified Systems truly ready for this?" Leon frowned. That comment was strange.

But before he could ask what the alien meant by that, Captain Anderson finally made his appearance in the Comms room.

"Good, you're both here. Kryik, I believe it's time we told the commander what's really going on here."

"This mission is far more than a simple shake-down run." Nihlus said bluntly. But the fact that Anderson apparently knew whatever it was that the Spectre was talking about calmed Leon down, just in time for Nihlus to turn around and look at him.

"I figured there was something that you weren't saying about this mission sir." This was directed to Anderson, who nodded.

"We're making a covert pick-up on Eden Prime. That's why we needed the stealth systems operational." Leon frowned slightly.

"There must be a reason you didn't tell me about this sooner sir."

"This comes down directly from the top. Information is listed as need-to-know basis only. I wanted to tell you, but until now..." Leon nodded once as Anderson trailed off.

"Until now I didn't need to know. It's understood sir. So what can I be told?"

"A team of Human archeologists on Eden Prime have discovered what they believe is a working Prothean beacon." This came from Nihlus, which made Shepard look back at him.

"Correct. And unfortunately, the researchers on Eden Prime do not have the kind of equipment necessary to study the beacon. So we're here to pick it up and bring it to the Citadel for proper study." Leon frowned at that but nodded to show his understanding. "This matter goes far beyond just human interests Shepard. It turns out that there is a standing Council law that all Prothean discoveries are to be shared with the Council so that the information garnered can be distributed to all races equally." Leon looked to Anderson as he spoke, then shrugged. He was just here to take orders. At least that's what he thought until...

"Of course, the beacon isn't the only reason I'm here." Shepard looked to Nihlus sharply, and if he was any judge at all, he could have sworn the Turian was grinning at him!

"Right. Nihlus is here to evaluate how you operate Shepard. The Union has been making a big push lately, and this is the result of it. We're being given an opportunity to get a Spectre." Leon's eyes widened as he turned to look at Anderson, who nodded once. Shepard took a moment to think, then turned to look at Nihlus.

"So you're to be what, my mentor and evaluator?"

"Correct. This will be the first of several missions that we will carry out together, intended for me to see how you operate on assignments of increasing stress levels. While retrieving the beacon is fairly important, there isn't much cause for concern with Eden Prime, so it will make an excellent starting point for our cooperation." Nihlus clasped his hands behind his back, one cheek rising in his grin again.

"Good. Now you two can get acquainted while I go find out what's keeping Moreau from patching us to -" Before Leon could finish his thought linking that name to Joker because of what Anderson had asked the pilot to do earlier, the intercom speaker above them flared to abrupt life.

"Uh, Captain? We've got a problem here. A big one. You're going to want to see this." All three men in the room frowned, while Leon muttered under his breath.

"So much for an easy start."

"Put whatever it is on the main screen in here Moreau."

"Roger that sir." The screen in the room flickered from the idyllic image of Eden Prime that Nihlus had been looking at, to one that showed the same landscape – but in a far, far darker light. There were flames guttering out near the outside of the city that Nihlus had been examining, with some rusty red splotches on the walls that Shepard's mind immediately associated with dried blood. His fear was confirmed when the camera panned around and they saw the body of a Union soldier lying on the ground, twisted around in death. The only sign of what had attacked them was a truly massive ship that was in the background – Leon would roughly estimate it as nearly twice the size of a destroyer, nearly the size of a full-on dreadnought. His mind boggled at that – ships above the size of a light frigate could not land on a planet!

"There's no one responding to any messages Captain. We're picking up signs of activity near the dig site, but there's some kind of interference that's breaking up the signal." Even as Joker spoker, the image on the screen started crackling, then froze in place, no longer a live feed. Leon turned to Anderson, who was already speaking.

"Gear up Commander. Whoever they are, they're here for the beacon. You're going to take a small squad and see if you can find out what's happened, and if possible, delay their absconding with the beacon. Do not let them take it Commander, dismissed!" Leon nodded sharply and began hurrying towards the elevator, barely noticing that Nihlus was keeping pace with him with those strangely bent legs that the Turians had. As they stepped into the elevator, Leon leaned against the wall and looked at him.

"Know anything about what that was?" He was disappointed when Nihlus shook his head.

"Never seen anything like that."_At least not that I can tell you. That looks like the thing that Saren and I found a few months ago. But that thing was dead in the water._ The Spectre crossed his arms as he looked at the elevator doors. "How do you plan on handling this?" Leon raised an eyebrow at him.

"You mean the ground insertion, not the overall situation. Right, I'm working off the assumption that while I'll receive info-updates from you I won't be able to give anything more than suggestions -" this got a nod from the Spectre, " so I'll be taking a small squad and landing as close as we possibly can to the dig site, make our way from there to the actual excavation zone, see if we can find any survivors or holdouts, or any signs of what exactly is attacking, or was if they're all gone. Eden _did_ have a defense contingent," Leon's eyes flickered at that. The contingent was just months away from full-scale homeworld status for Earth, which would have given them the rights to three Evangelion units, which might have been enough to save the people here. When he got back to Humanspace he'd have to send a message in suggesting that the population cap be lowered, or talk Anderson into doing it... He shook his head and refocused on Nihlus.

"Sorry. Right, they had a defense contingent, which should have been able to take out at least a few of the assailants, or hopefully left some kind of data about them." Leon looked over to Nihlus, and the Human cursed his difficulty in reading the Turian facial structure. The other soldier was simply staring at him – then those strange, plated cheeks spread wider, baring a few of his teeth.

"And if you find any of these mystery assailants?"

"We obliterate them." Shepard's voice could have frozen plasma. For a moment the man was back on that dusty red planet, the screams of his dying teammates filling his ears. In that moment, when he looked at Nihlus, he didn't see the Spectre – he saw Corporal Toombs, his bunkpartner and the man he had gone through Pilot qualifications with. But then the moment was over as the elevator's doors _finally_ dinged and slid open, revealing the austere environment of the hangar bay where the armory and the shuttles were kept. Shepard saw that his two normal teammates for ground missions – Lieutenant Kaiden Alenko and Sargent Jace Allen were already there, kitted up and holding their M-8 Avengers in their hands. Kaiden's preferred secondary, a moderately powerful Tempest SMG was maglocked onto his hip, while Allen's shotgun could be seen locked to the small of his back.

"Right guys. We're going in hot on this one. No knowledge of who exactly our opposition is, so be prepared for anything. Allen, you grew up here, right?" As Leon spoke he was stepping out of the elevator, flanked by Nihlus who for the moment seemed to be content just to listen. The two moved to the armory lockers, with Shepard pulling out the tried and true Vindicator assault rifle that he preferred for his primary, while he went with a Viper for his sniper rifle. He'd have rather taken a Mantis down, but for this the higher number of shots before venting would be more versatile. He settled for just these two as he heard the Sargent speak.

"Right commander. No clue what it is that's brought these rats here. Eden Prime's an agri-world primarily. I mean yeah, we have the ruins that has a team half-heartedly rooting through it, but we're far from the only one that has something like that. Except for the Marine detachment we're not likely to have any support even if there are colonists alive. Most of them are going to be absolutely terrified, and taking them with us would just end up slowing us down. Sorry sir, I know you were hoping for reinforcements." That just showed how much the three of them had gotten to know each other in just the few short weeks that they'd been together. Shepard had a very drastic appreciation for, as he called it, 'overwhelming numbers of people who'll shoot anything that twitches wrong.' Strangely, at least to Jace and Kaiden, Shepard shook his head.

"That's actually a good thing." That was an unusual comment for them to hear, but Shepard didn't expand on it. Shepard straightened up and looked to his team.

"Right. We're a strike force for this operation. We're not here to draw attention – the Normandy, despite being a standard frigate, would _not_ be able to take that thing on. So we're going to do our best to find out what's going on, and if at all possible, recover the original target for our coming here. Quick quiet and clean gentlemen. Let's go." Leon picked up his helmet and sealed it in place, the face guard sliding up to cover his scarred visage, then stepped onto the shuttle that would take them to the surface, unaware that what would happen today would become the basis of many, many changes between Humanity and its sister races in the galaxy.

_**AN: Well. I don't know how well this will be accepted, but I hope everyone who reads it will enjoy it!**_

_**Also, this is unbetaed, so apologies for any big mistakes that I missed.**_

_**Jet out!**_


End file.
